A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks

Table 3 Reaction network of the heat shock response model.

RxnNo.	Reactions	Rate const	Reaction Type
1	Protein → UnfProt	0.2	Unfolding
2	UnfProt + DnaJ → UnfProt:DnaJ	0.0108	Association
3	UnfProt:DnaJ → Protein + DnaJ	0.2	Dissociation/Folding
4	DNA(σ32) → mRNA(σ32)	1.40E-03	Transcription
5	mRNA(σ32) → σ32	0.07	Translation
6	mRNA(σ32) → degrades	1.40E-06	Degradation
7	σ32 → σ32_RNAP	0.7	Conformational
8	σ32_RNAP → σ32	1.3E-01	Conformational
9	DNA(DnaJ) + σ32_RNAP → DNA(DnaJ) + σ32 + DnaJ	4.88E-03	Transcription combined with Translation
10	DNA(FtsH) + σ32_RNAP → DNA(FtsH) + σ32 + FtsH	4.88E-03
11	DNA(GroEL) + σ32_RNAP → DNA(GroEL) + σ32 + GroEL	6.29E-03
12	DnaJ → degrades	6.40E-10	Degradation
13	FtsH → degrades	7.40E-11
14	GroEL → degrades	1.80E-08
15	σ32 + DnaJ → σ32:DnaJ	3.62E-04	Association
16	σ32:DnaJ → σ32 + DnaJ	4.40E-04	Dissociation
17	FtsH + σ32:DnaJ → DnaJ + FtsH	1.42E-06

The units of stochastic rate constants are s^-1 for 1^st-order reactions and (molecule-s)^-1 for 2^nd-order reactions. DNA(X) and mRNA(X) correspond to DNA sequence and mRNA transcripts, respectively, for species X. DNA (or mRNA) molecules do not get consumed in the transcription (or translation) reactions, but simply provide a template for mRNA (or protein) formation.

ISSN: 1471-2105